Demo Data from EDBT 2026 / reviewers in the wild / expert
Satrio Wibowo
dblp:425/2646
· DBLP profile ↗
1ranked-venue papers
0as first author
1since 2021 · last 2024
0000-0002-8892-3808ORCID · reported
Domains — the database's venue-derived domains; a paper can count in several
Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021
Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.
| Interdisciplinary, comprehensive, and emerging computing
1 paper |
Bioinformatics and computational biology · 100% |
Topics — the 2 heaviest of 2, each with the papers that count most for it
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Bioinformatics and computational biology › sequence analysis
nanopore sequencing |
0.8 | 1 | 2024 | Icarust, a real-time simulator for Oxford Nanopore adaptive sampling · Bioinform. 2024 |
Bioinformatics and computational biology
sequencing simulation |
0.8 | 1 | 2024 | Icarust, a real-time simulator for Oxford Nanopore adaptive sampling · Bioinform. 2024 |
Methods — techniques the papers use, named apart from their topics
rust · 0.8docker · 0.8
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2024 | Icarust, a real-time simulator for Oxford Nanopore adaptive samplingabstractMOTIVATION: Oxford Nanopore Technologies (ONT) sequencers enable real-time generation of sequence data, which allows for concurrent analysis during a run. Adaptive sampling leverages this real-time capability in extremis, rejecting or accepting reads for sequencing based on assessment of the sequence from the start of each read. This functionality is provided by ONT's software, MinKNOW (Oxford Nanopore Technologies). Designing and developing software to take advantage of adaptive sampling can be costly in terms of sequencing consumables, using precious samples and preparing sequencing libraries. MinKNOW addresses this in part by allowing the replay of previously sequenced runs for testing. However, as we show, the sequencing output only partially changes in response to adaptive sampling instructions. Here we present Icarust, a tool enabling more accurate approximations of sequencing runs. Icarust recreates all the required endpoints of MinKNOW to perform adaptive sampling and writes output compatible with current base-callers and analysis pipelines. Icarust serves nanopore signal simulating a MinION or PromethION flow cell experiment from any reference genome using either R9 or R10 pore models. We show that simulating sequencing runs with Icarust provides a realistic testing and development environment for software exploiting the real-time nature of Nanopore sequencing. AVAILABILITY AND IMPLEMENTATION: All code is open source and freely available here-https://github.com/LooseLab/Icarust. Icarust is implemented in Rust, with a docker container also available. The data underlying this article will be shared on reasonable request to the corresponding author. Rory Munro, Satrio Wibowo, Alexander Payne, Matthew Loose |
Bioinform. | 2 |